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settings.yml
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settings.yml
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############
# Funnotate
############
# Table of gene families, from LIS data store
gene_families_data: https://data.legumeinfo.org/LEGUMES/Fabaceae/genefamilies/mixed.fam1.M65K/legume.mixed.fam1.M65K.info_annot_ahrd.tsv.gz
# General settings
num_threads: 5
# error_log: [...]
# ESTScan
estscan:
exe: /falafel/funnotate/estscan-3.0.3/estscan
matrix: /falafel/funnotate/smat/medicago.smat
# BLAST: expects the databases in indexed format (.phr, .pin, .psq)
blast:
exe: /falafel/adf/e00/adf/blast-2.2.23/bin/blastall
# To use blastp [...] instead of blastall -p blastp [...],
# exe: /usr/bin/blastp
dbs:
- /falafel/funnotate/blast-dbs/TAIR10_pep_20101209
- /falafel/funnotate/blast-dbs/Glyma.refseq_protein.fasta
- /falafel/funnotate/blast-dbs/Mt4.0v1_GenesProteinSeq_20130731_1800.fasta
# AHRD
ahrd:
java: /usr/bin/java
jar: /falafel/funnotate/AHRD/ahrd.jar
yml: /falafel/funnotate/AHRD/ahrd_nosp.yml
# InterPro
interpro:
exe: /falafel/adf/sw/interproscan-5.3-46.0/interproscan-java1.7.sh
params: -appl TIGRFAM,SMART,SUPERFAMILY,Gene3D,PIRSF,Pfam,Coils
# HMMer
hmmer:
exe: /falafel/adf/sw/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmscan
db: /falafel/funnotate/hmmdb/legfed_v1_0/legfed_v1_0.hmm
# Unused:
# params: [...]
# target_families: [...]/07_family_fasta
# Lorax
lorax:
url: 127.0.0.1:9100
# args: [...]
############